[ENH] Replace local graph data with volume

Addresses #55
neurobagel · May 14, 2024 · 59cb11f · 59cb11f
1 parent 2f64814
commit 59cb11f
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -32,15 +32,14 @@ services:
       - "local_node_query"
       - "full_stack"
     volumes:
-      - "${NB_GRAPH_ROOT_HOST:-~/graphdb-home}:${NB_GRAPH_ROOT_CONT:-/opt/graphdb/home}"
+      - "graph_data:/opt/graphdb/home"
       - "./scripts:/usr/src/neurobagel/scripts"
       - ".env:/usr/src/neurobagel/.env"
       - "./vocab:/usr/src/neurobagel/vocab"
       - "${LOCAL_GRAPH_DATA:-./data}:/data"
     ports:
       - "${NB_GRAPH_PORT_HOST:-7200}:${NB_GRAPH_PORT:-7200}"
     environment:
-      NB_GRAPH_ROOT_CONT: ${NB_GRAPH_ROOT_CONT:-/opt/graphdb/home}
       NB_GRAPH_USERNAME: ${NB_GRAPH_USERNAME}
       NB_GRAPH_ADDRESS: ${NB_GRAPH_ADDRESS:-graph}
       NB_GRAPH_PORT: ${NB_GRAPH_PORT:-7200}
@@ -89,4 +88,7 @@ secrets:
   db_admin_password:
     environment: "NB_GRAPH_ADMIN_PASSWORD"
   db_user_password:
-    environment: "NB_GRAPH_PASSWORD"
+    environment: "NB_GRAPH_PASSWORD"
+
+volumes:
+  graph_data:
diff --git a/docs/neurobagel_environment_variables.tsv b/docs/neurobagel_environment_variables.tsv
@@ -15,8 +15,6 @@ Environment variable	Set manually in .env?	Description	Default value if not set
 `NB_FAPI_PORT`	No	Port number on which to run the Neurobagel federation API _in the API container_	`8000`	Docker
 `NB_GRAPH_IMG`	No	Graph server Docker image	`ontotext/graphdb:10.3.1`	Docker
 `NB_GRAPH_ADDRESS`	No	IP address for the graph database (or container name, if graph is hosted locally)	`206.12.99.17 (graph)` **	Docker, Python
-`NB_GRAPH_ROOT_HOST`	No	Path to directory on the _host machine_ to store graph database files and data (directory does not have to exist beforehand).	`~/graphdb-home`	Docker
-`NB_GRAPH_ROOT_CONT`	No	Path to directory for graph databases in the _graph server container_	`/opt/graphdb/home` *	Docker
 `NB_GRAPH_PORT_HOST`	No	Port number on the _host machine_ to map the graph server container port to	`7200`	Docker
 `NB_GRAPH_PORT`	No	Port number used by the _graph server container_	`7200` *	Docker, Python
 `NB_QUERY_TAG`	No	Docker image tag for the query tool	`latest`	Docker

diff --git a/scripts/setup.sh b/scripts/setup.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-/opt/graphdb/dist/bin/graphdb -Dgraphdb.home=${NB_GRAPH_ROOT_CONT} &
+/opt/graphdb/dist/bin/graphdb -Dgraphdb.home=/opt/graphdb/home &
 GRAPHDB_PID=$!
 
 export NB_GRAPH_ADMIN_PASSWORD=$(cat /run/secrets/db_admin_password)